1F7V

CRYSTAL STRUCTURE OF YEAST ARGINYL-TRNA SYNTHETASE COMPLEXED WITH THE TRNAARG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

tRNA aminoacylation by arginyl-tRNA synthetase: induced conformations during substrates binding

Delagoutte, B.Moras, D.Cavarelli, J.

(2000) EMBO J. 19: 5599-5610

  • DOI: 10.1093/emboj/19.21.5599
  • Primary Citation of Related Structures:  1F7U

  • PubMed Abstract: 
  • The 2.2 A crystal structure of a ternary complex formed by yeast arginyl-tRNA synthetase and its cognate tRNA(Arg) in the presence of the L-arginine substrate highlights new atomic features used for specific substrate recognition. This first example ...

    The 2.2 A crystal structure of a ternary complex formed by yeast arginyl-tRNA synthetase and its cognate tRNA(Arg) in the presence of the L-arginine substrate highlights new atomic features used for specific substrate recognition. This first example of an active complex formed by a class Ia aminoacyl-tRNA synthetase and its natural cognate tRNA illustrates additional strategies used for specific tRNA selection. The enzyme specifically recognizes the D-loop and the anticodon of the tRNA, and the mutually induced fit produces a conformation of the anticodon loop never seen before. Moreover, the anticodon binding triggers conformational changes in the catalytic center of the protein. The comparison with the 2.9 A structure of a binary complex formed by yeast arginyl-tRNA synthetase and tRNA(Arg) reveals that L-arginine binding controls the correct positioning of the CCA end of the tRNA(Arg). Important structural changes induced by substrate binding are observed in the enzyme. Several key residues of the active site play multiple roles in the catalytic pathway and thus highlight the structural dynamics of the aminoacylation reaction.


    Related Citations: 
    • Crystallization and preliminary X-ray crystallographic analysis of yeast arginyl-tRNA synthetase - yeast tRNAArg complexes
      Delagoutte, B.,Keith, G.,Moras, D.,Cavarelli, J.
      (2000) Acta Crystallogr.,Sect.D 56: 492


    Organizational Affiliation

    UPR 9004 Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, BP 163, 67404 Illkirch Cedex, France. cava@igbmc.u-strasbg.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ARGINYL-TRNA SYNTHETASE
A
607Saccharomyces cerevisiae (strain ATCC 204508 / S288c)EC: 6.1.1.19
Find proteins for Q05506 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q05506
Entity ID: 1
MoleculeChainsLengthOrganism
TRNA(ARG)B76N/A
Small Molecules
Modified Residues  8 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
B
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
B
RNA LINKINGC10 H16 N3 O8 PC
1MG
Query on 1MG
B
RNA LINKINGC11 H16 N5 O8 PG
M2G
Query on M2G
B
RNA LINKINGC12 H18 N5 O8 PG
1MA
Query on 1MA
B
RNA LINKINGC11 H16 N5 O7 PA
2MG
Query on 2MG
B
RNA LINKINGC11 H16 N5 O8 PG
5MU
Query on 5MU
B
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
B
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.194 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 107.721α = 90.00
b = 129.606β = 90.00
c = 184.006γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-06-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance